EMDB-50292: Structure of Pol II-TC-NER-STK19 complex, consensus map

Basic information

Entry

Database: EMDB / ID: EMD-50292

• Title: Structure of Pol II-TC-NER-STK19 complex, consensus map
• Map data: raw map

Sample

• Complex: Ternary complex of Pol II-TC-NER-STK19, consensus map
  • Protein or peptide: x 22 types
  • DNA: x 2 types
  • RNA: x 1 types

• Keywords: Transcription-coupled DNA repair / TRANSCRIPTION

Function / homology

Function:

RNA polymerase inhibitor activity / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / positive regulation of single strand break repair / response to auditory stimulus / regulation of transcription elongation by RNA polymerase II / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / B-WICH complex / cullin-RING ubiquitin ligase complex / DNA protection / single strand break repair / cellular response to chemical stress / regulation of DNA damage checkpoint / Cul7-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / chromatin-protein adaptor activity / response to superoxide / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / photoreceptor cell maintenance / regulation of nucleotide-excision repair / ATP-dependent chromatin remodeler activity / epigenetic programming in the zygotic pronuclei / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / nuclear lumen / protein neddylation / UV-damage excision repair / positive regulation of Ras protein signal transduction / response to UV-B / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / positive regulation of transcription by RNA polymerase III / SCF ubiquitin ligase complex / WD40-repeat domain binding / Cul2-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / ATP-dependent DNA damage sensor activity / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of transcription by RNA polymerase I / TGF-beta receptor signaling activates SMADs / RNA polymerase II complex binding / cullin family protein binding / hemopoiesis / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein tyrosine kinase activator activity / viral release from host cell / RNA Polymerase I Transcription Initiation / site of DNA damage / regulation of proteolysis / regulation of postsynapse assembly / pyrimidine dimer repair / somatic stem cell population maintenance / anatomical structure morphogenesis / protein monoubiquitination / response to X-ray / ATP-dependent activity, acting on DNA / positive regulation of G1/S transition of mitotic cell cycle

Domain/homology:

Serine-threonine protein kinase 19 / Inactive serine-threonine protein kinase 19 / UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / : / Nedd8-like ubiquitin / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / ENTH/VHS / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb4/RPC9, core / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11

Component:

DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / Winged helix repair factor 1 / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase II subunit RPB9 / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-6 / DNA excision repair protein ERCC-8 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A / DET1- and DDB1-associated protein 1

• Biological species: Homo sapiens (human) / Sus scrofa domesticus (domestic pig)
• Method: single particle reconstruction / cryo EM / Resolution: 4.2 Å
• Authors: Lee S-H / Sixma TK

Funding support

Netherlands, 2 items

Organization	Grant number	Country
Netherlands Organisation for Scientific Research (NWO)	TOP 714.017.003	Netherlands
Oncode Institute		Netherlands

• Citation: Journal: Mol Cell / Year: 2024; Title: STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment.; Authors: Anisha R Ramadhin / Shun-Hsiao Lee / Di Zhou / Anita Salmazo / Camila Gonzalo-Hansen / Marjolein van Sluis / Cindy M A Blom / Roel C Janssens / Anja Raams / Dick Dekkers / Karel Bezstarosti / Dea Slade / Wim Vermeulen / Alex Pines / Jeroen A A Demmers / Carrie Bernecky / Titia K Sixma / Jurgen A Marteijn / ; Abstract: Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4 ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4 serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4 activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4 activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component.

History

Deposition	May 14, 2024	-
Header (metadata) release	Nov 13, 2024	-
Map release	Nov 13, 2024	-
Update	Jan 8, 2025	-
Current status	Jan 8, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_50292.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: raw map
• Voxel size: X=Y=Z: 1.06 Å

Density

Contour Level	By AUTHOR: 0.12
Minimum - Maximum	-0.26970944 - 0.6987728
Average (Standard dev.)	0.0006491148 (±0.020178651)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 423.99997 Å α=β=γ: 90.0 °

Supplemental data

Half map: half map B

• File: emd_50292_half_map_1.map
• Annotation: half map B

Half map: half map A

• File: emd_50292_half_map_2.map
• Annotation: half map A

Sample components

Entire : Ternary complex of Pol II-TC-NER-STK19, consensus map

• Entire: Name: Ternary complex of Pol II-TC-NER-STK19, consensus map

Components

• Complex: Ternary complex of Pol II-TC-NER-STK19, consensus map
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4
  • Protein or peptide: DNA-directed RNA polymerase II subunit E
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
  • Protein or peptide: DNA-directed RNA polymerase subunit RPB7
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-a
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
  • Protein or peptide: DNA excision repair protein ERCC-8
  • Protein or peptide: DNA damage-binding protein 1
  • Protein or peptide: DET1- and DDB1-associated protein 1
  • Protein or peptide: UV-stimulated scaffold protein A
  • Protein or peptide: DNA excision repair protein ERCC-6
  • Protein or peptide: Transcription elongation factor 1 homolog
  • Protein or peptide: Inactive serine/threonine-protein kinase 19
  • Protein or peptide: Cullin-4A
  • Protein or peptide: E3 ubiquitin-protein ligase RBX1
  • Protein or peptide: NEDD8
  • DNA: Template strand DNA
  • DNA: Non-template strand DNA
  • RNA: RNA

Supramolecule #1: Ternary complex of Pol II-TC-NER-STK19, consensus map

• Supramolecule: Name: Ternary complex of Pol II-TC-NER-STK19, consensus map / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 1.17 MDa

Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTG RCQTCAGNMT ECPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV D SNNPKIKD ILAKSKGQPK KRLTHVYDLC KGKNICEGGE EMDNKFGVEQ PEGDEDLTKE KG HGGCGRY QPRIRRSGLE LYAEWKHVNE DSQEKKILLS PERVHEIFKR ISDEECFVLG MEP RYARPE WMIVTVLPVP PLSVRPAVVM QGSARNQDDL THKLADIVKI NNQLRRNEQN GAAA HVIAE DVKLLQFHVA TMVDNELPGL PRAMQKSGRP LKSLKQRLKG KEGRVRGNLM GKRVD FSAR TVITPDPNLS IDQVGVPRSI AANMTFAEIV TPFNIDRLQE LVRRGNSQYP GAKYII RDN GDRIDLRFHP KPSDLHLQTG YKVERHMCDG DIVIFNRQPT LHKMSMMGHR VRILPWS TF RLNLSVTTPY NADFDGDEMN LHLPQSLETR AEIQELAMVP RMIVTPQSNR PVMGIVQD T LTAVRKFTKR DVFLERGEVM NLLMFLSTWD GKVPQPAILK PRPLWTGKQI FSLIIPGHI NCIRTHSTHP DDEDSGPYKH ISPGDTKVVV ENGELIMGIL CKKSLGTSAG SLVHISYLEM GHDITRLFY SNIQTVINNW LLIEGHTIGI GDSIADSKTY QDIQNTIKKA KQDVIEVIEK A HNNELEPT PGNTLRQTFE NQVNRILNDA RDKTGSSAQK SLSEYNNFKS MVVSGAKGSK IN ISQVIAV VGQQNVEGKR IPFGFKHRTL PHFIKDDYGP ESRGFVENSY LAGLTPTEFF FHA MGGREG LIDTAVKTAE TGYIQRRLIK SMESVMVKYD ATVRNSINQV VQLRYGEDGL AGES VEFQN LATLKPSNKA FEKKFRFDYT NERALRRTLQ EDLVKDVLSN AHIQNELERE FERMR EDRE VLRVIFPTGD SKVVLPCNLL RMIWNAQKIF HINPRLPSDL HPIKVVEGVK ELSKKL VIV NGDDPLSRQA QENATLLFNI HLRSTLCSRR MAEEFRLSGE AFDWLLGEIE SKFNQAI AH PGEMVGALAA QSLGEPATQM TLNTFHYAGV SAKNVTLGVP RLKELINISK KPKTPSLT V FLLGQSARDA ERAKDILCRL EHTTLRKVTA NTAIYYDPNP QSTVVAEDQE WVNVYYEMP DFDVARISPW LLRVELDRKH MTDRKLTMEQ IAEKINAGFG DDLNCIFNDD NAEKLVLRIR IMNSDENKM QEEEEVVDKM DDDVFLRCIE SNMLTDMTLQ GIEQISKVYM HLPQTDNKKK I IITEDGEF KALQEWILET DGVSLMRVLS EKDVDPVRTT SNDIVEIFTV LGIEAVRKAL ER ELYHVIS FDGSYVNYRH LALLCDTMTC RGHLMAITRH GVNRQDTGPL MKCSFEETVD VLM EAAAHG ESDPMKGVSE NIMLGQLAPA GTGCFDLLLD AEKCKYGMEI PTNIPGLGAA GPTG MFFGS APSPMGGISP AMTPWNQGAT PAYGAWSPSV GSGMTPGAAG FSPSAASDAS GFSPG YSPA WSPTPGSPGS PGPSSPYIPS PGGAMSPSYS PTSPAYEPRS PGGYTPQSPS YSPTSP SYS PTSPSYSPTS PNYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSP TS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPS Y SPTSPNYSPT SPNYTPTSPS YSPTSPSYSP TSPNYTPTSP NYSPTSPSYS PTSPSYSPT SPSYSPSSPR YTPQSPTYTP SSPSYSPSSP SYSPTSPKYT PTSPSYSPSS PEYTPTSPKY SPTSPKYSP TSPKYSPTSP TYSPTTPKYS PTSPTYSPTS PVYTPTSPKY SPTSPTYSPT S PKYSPTSP TYSPTSPKGS TYSPTSPGYS PTSPTYSLTS PAISPDDSDE EN

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MKPLRPENPP KAELKGLLFV QQHCKTRLHS VAVTRPRGAA TEESTPKLRM CSTNLSQALA YFRAGANLTA ASLWAGFRGS RRIFWERRKR KSLCLALRPG GACWRWLLAV SCVSLRGLGA PGSCANMYDA DEDMQYDEDD DEITPDLWQE ACWIVISSYF DEKGLVRQQL DSFDEFIQMS VQRIVEDAPP IDLQAEAQHA SGEVEEPPRY LLKFEQIYLS KPTHWERDGA PSPMMPNEAR LRNLTYSAPL YVDITKTVIK EGEEQLQTQH QKTFIGKIPI MLRSTYCLLN GLTDRDLCEL NECPLDPGGY FIINGSEKVL IAQEKMATNT VYVFAKKDSK YAYTGECRSC LENSSRPTST IWVSMLARGG QGAKKSAIGQ RIVATLPYIK QEVPIIIVFR ALGFVSDRDI LEHIIYDFED PEMMEMVKPS LDEAFVIQEQ NVALNFIGSR GAKPGVTKEK RIKYAKEVLQ KEMLPHVGVS DFCETKKAYF LGYMVHRLLL AALGRRELDD RDHYGNKRLD LAGPLLAFLF RGMFKNLLKE VRIYAQKFID RGKDFNLELA IKTRIISDGL KYSLATGNWG DQKKAHQARA GVSQVLNRLT FASTLSHLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLVK NLALMAYISV GSQPSPILEF LEEWSMENLE EISPAAIADA TKIFVNGCWV GIHKDPEQLM NTLRKLRRQM DIIVSEVSMI RDIREREIRI YTDAGRICRP LLIVEKQKLL LKKRHIDQLK EREYNNYSWQ DLVASGVVEY IDTLEEETVM LAMTPDDLQE KEVAYCSTYT HCEIHPSMIL GVCASIIPFP DHNQSPRNTY QSAMGKQAMG VYITNFHVRM DTLAHVLYYP QKPLVTTRSM EYLRFRELPA GINSIVAIAS YTGYNQEDSV IMNRSAVDRG FFRSVFYRSY KEQESKKGFD QEEVFEKPTR ETCQGMRHAI YDKLDDDGLI APGVRVSGDD VIIGKTVTLP ENEDELEGTN RRYTKRDCST FLRTSETGIV DQVMVTLNQE GYKFCKIRVR SVRIPQIGDK FASRHGQKGT CGIQYRQEDM PFTCEGITPD IIINPHAIPS RMTIGHLIEC LQGKVSANKG EIGDATPFND AVNVQKISNL LSDYGYHLRG NEVLYNGFTG RKITSQIFIG PTYYQRLKHM VDDKIHSRAR GPIQILNRQP MEGRSRDGGL RFGEMERDCQ IAHGAAQFLR ERLFEASDPY QVHVCNLCGI MAIANTRTHT YECRGCRNKT QISLVRMPYA CKLLFQELMS MSIAPRMMSV

UniProtKB: DNA-directed RNA polymerase subunit beta

Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR LRAYAKKGFG KEHAKWNPTA GVAFEYDPDN ALRHTVYPKP EEWPKSEYSE LDEDESQAPY DPNGKPERFY YNVESCGSLR PETIVLSALS GLKKKLSDLQ TQLSHEIQSD VLTIN

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL ANLCPETAEE SKALIPSLEG RFEDEELQQI LDDIQTKRSF QY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

Macromolecule #5: DNA-directed RNA polymerase II subunit E

• Macromolecule: Name: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL ARYKLRENQL PRIQAGDPVA RYFGIKRGQV VKIIRPSETA GRYITYRLVQ

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC2; type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDPL LIAMKELKAR KIPIIIRRYL PDGSYEDWGV DELIISD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

Macromolecule #7: DNA-directed RNA polymerase subunit RPB7

• Macromolecule: Name: DNA-directed RNA polymerase subunit RPB7 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVVT QVNKVGLFTE IGPMSCFISR HSIPSEMEFD PNSNPPCYKT MDEDIVIQQD DEIRLKIVGT RVDKNDIFAI GSLMDDYLGL VS

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC3; type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFEY VMYGKVYRIE GDETSTEAAT RLSAYVSYGG LLMRLQGDAN NLHGFEVDSR VYLLMKKLAF

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKCG HKEAVFFQSH SARAEDAMRL YYVCTAPHCG HRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC5; type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTNA ITDLISELSL LEERFRVAIK DKQEGIE

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC4; type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa domesticus (domestic pig) / Organ: thymus

Sequence

String:

MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

Macromolecule #13: DNA excision repair protein ERCC-8

• Macromolecule: Name: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 13 ; Details: The construct contains a Strep tag II at the C-terminus; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCSI GRDHPDVHRY SVETVQWYPH DTGMFTSSSF DKTLKVWDTN TLQTADVFNF EETVYSHHMS PVSTKHCLVA VGTRGPKVQL CDLKSGSCSH ILQGHRQEIL AVSWSPRYDY ILATASADSR VKLWDVRRAS GCLITLDQHN GKKSQAVESA NTAHNGKVNG LCFTSDGLHL LTVGTDNRMR LWNSSNGENT LVNYGKVCNN SKKGLKFTVS CGCSSEFVFV PYGSTIAVYT VYSGEQITML KGHYKTVDCC VFQSNFQELY SGSRDCNILA WVPSLYEPVP DDDETTTKSQ LNPAFEDAWS SSDEEGGTSA WSHPQFEK

UniProtKB: DNA excision repair protein ERCC-8

Macromolecule #14: DNA damage-binding protein 1

• Macromolecule: Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 14 / Details: The construct contains a His tag at the N-terminus / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPNRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF ACSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT IGTIDEIQKL HIRTVPLYES PRKICYQEVS QCFGVLSSRI EVQDTSGGTT ALRPSASTQA LSSSVSSSKL FSSSTAPHET SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN PNWMSAVEIL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGET STPTQGSVLF GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH

UniProtKB: DNA damage-binding protein 1

Macromolecule #15: DET1- and DDB1-associated protein 1

• Macromolecule: Name: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 15 ; Details: The construct contains a twin Strep tag and a flag tag at the C-terminus; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRKV ARTDSPDMHE DTDVLFQGPG AWSHPQFEKG GGSGGGSGGG SWSHPQFEKG ASGEDYKDDD DK

UniProtKB: DET1- and DDB1-associated protein 1

Macromolecule #16: UV-stimulated scaffold protein A

• Macromolecule: Name: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 16 / Details: The construct contains a His tag at the N-terminus / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLELT LGTDPAQPLP PPREAAQRLR QATTRAVEGW NEKFGEAYKK LALGYHFLRH NKKVDFQDTN ARSLAERKRE EEKQKHLDKI YQERASQAER EMQEMSGEIE SCLTEVESCF RLLVPFDFDP NPETESLGMA SGMSDALRSS CAGQVGPCRS GTPDPRDGEQ PCCSRDLPAS AGHPRAGGGA QPSQTATGDP SDEDEDSDLE EFVRSHGLGS HKYTLDVELC SEGLKVQENE DNLALIHAAR DTLKLIRNKF LPAVCSWIQR FTRVGTHGGC LKRAIDLKAE LELVLRKYKE LDIEPEGGER RRTEALGDAE EDEDDEDFVE VPEKEGYEPH IPDHLRPEYG LEAAPEKDTV VRCLRTRTRM DEEVSDPTSA AAQLRQLRDH LPPPSSASPS RALPEPQEAQ KLAAERARAP VVPYGVDLHY WGQELPTAGK IVKSDSQHRF WKPSEVEEEV VNADISEMLR SRHITFAGKF EPVQHWCRAP RPDGRLCERQ DRLKCPFHGK IVPRDDEGRP LDPEDRAREQ RRQLQKQERP EWQDPELMRD VEAATGQDLG SSRYSGKGRG KKRRYPSLTN LKAQADTARA RIGRKVFAKA AVRRVVAAMN RMDQKKHEKF SNQFNYALN

UniProtKB: UV-stimulated scaffold protein A

Macromolecule #17: DNA excision repair protein ERCC-6

• Macromolecule: Name: DNA excision repair protein ERCC-6 / type: protein_or_peptide / ID: 17 ; Details: The construct contains a N-terminal HA tag and a C-terminal His tag; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MPNEGIPHSS QTQEQDCLQS QPVSNNEEMA IKQESGGDGE VEEYLSFRSV GDGLSTSAVG CASAAPRRGP ALLHIDRHQI QAVEPSAQAL ELQGLGVDVY DQDVLEQGVL QQVDNAIHEA SRASQLVDVE KEYRSVLDDL TSCTTSLRQI NKIIEQLSPQ AATSRDINRK LDSVKRQKYN KEQQLKKITA KQKHLQAILG GAEVKIELDH ASLEEDAEPG PSSLGSMLMP VQETAWEELI RTGQMTPFGT QIPQKQEKKP RKIMLNEASG FEKYLADQAK LSFERKKQGC NKRAARKAPA PVTPPAPVQN KNKPNKKARV LSKKEERLKK HIKKLQKRAL QFQGKVGLPK ARRPWESDMR PEAEGDSEGE ESEYFPTEEE EEEEDDEVEG AEADLSGDGT DYELKPLPKG GKRQKKVPVQ EIDDDFFPSS GEEAEAASVG EGGGGGRKVG RYRDDGDEDY YKQRLRRWNK LRLQDKEKRL KLEDDSEESD AEFDEGFKVP GFLFKKLFKY QQTGVRWLWE LHCQQAGGIL GDEMGLGKTI QIIAFLAGLS YSKIRTRGSN YRFEGLGPTV IVCPTTVMHQ WVKEFHTWWP PFRVAILHET GSYTHKKEKL IRDVAHCHGI LITSYSYIRL MQDDISRYDW HYVILDEGHK IRNPNAAVTL ACKQFRTPHR IILSGSPMQN NLRELWSLFD FIFPGKLGTL PVFMEQFSVP ITMGGYSNAS PVQVKTAYKC ACVLRDTINP YLLRRMKSDV KMSLSLPDKN EQVLFCRLTD EQHKVYQNFV DSKEVYRILN GEMQIFSGLI ALRKICNHPD LFSGGPKNLK GLPDDELEED QFGYWKRSGK MIVVESLLKI WHKQGQRVLL FSQSRQMLDI LEVFLRAQKY TYLKMDGTTT IASRQPLITR YNEDTSIFVF LLTTRVGGLG VNLTGANRVV IYDPDWNPST DTQARERAWR IGQKKQVTVY RLLTAGTIEE KIYHRQIFKQ FLTNRVLKDP KQRRFFKSND LYELFTLTSP DASQSTETSA IFAGTGSDVQ TPKCHLKRRI QPAFGADHDV PKRKKFPASN ISVNDATSSE EKSEAKGAEV NAVTSNRSDP LKDDPHMSSN VTSNDRLGEE TNAVSGPEEL SVISGNGECS NSSGTGKTSM PSGDESIDEK LGLSYKRERP SQAQTEAFWE NKQMENNFYK HKSKTKHHSV AEEETLEKHL RPKQKPKNSK HCRDAKFEGT RIPHLVKKRR YQKQDSENKS EAKEQSNDDY VLEKLFKKSV GVHSVMKHDA IMDGASPDYV LVEAEANRVA QDALKALRLS RQRCLGAVSG VPTWTGHRGI SGAPAGKKSR FGKKRNSNFS VQHPSSTSPT EKCQDGIMKK EGKDNVPEHF SGRAEDADSS SGPLASSSLL AKMRARNHLI LPERLESESG HLQEASALLP TTEHDDLLVE MRNFIAFQAH TDGQASTREI LQEFESKLSA SQSCVFRELL RNLCTFHRTS GGEGIWKLKP EYC

UniProtKB: DNA excision repair protein ERCC-6

Macromolecule #18: Transcription elongation factor 1 homolog

• Macromolecule: Name: Transcription elongation factor 1 homolog / type: protein_or_peptide / ID: 18 ; Details: The first two residues (Gly, Ala) are residual residues after TEV protease treatment. ELOF1 sequence starts from residue 3 (Met).; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GAMGRRKSKR KPPPKKKMTG TLETQFTCPF CNHEKSCDVK MDRARNTGVI SCTVCLEEFQ TPITYLSEPV DVYSDWIDAC EAANQ

UniProtKB: Transcription elongation factor 1 homolog

Macromolecule #19: Inactive serine/threonine-protein kinase 19

• Macromolecule: Name: Inactive serine/threonine-protein kinase 19 / type: protein_or_peptide / ID: 19 ; Details: The first three residues (Gly, Pro, Gly) are residual residues after 3C protease treatment. The coding sequence of STK19 starts from residue 4 (Met).; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

GPGMSWKRHH LIPETFGVKR RRKRGPVESD PLRGEPGSAR AAVSELMQLF PRGLFEDALP PIVLRSQVYS LVPDRTVADR QLKELQEQGE IRIVQLGFDL DAHGIIFTED YRTRVLKACD GRPYAGAVQK FLASVLPACG DLSFQQDQMT QTFGFRDSEI THLVNAGVLT VRDAGSWWLA VPGAGRFIKY FVKGRQAVLS MVRKAKYREL LLSELLGRRA PVVVRLGLTY HVHDLIGAQL VDCISTTSGT LLRLPET

UniProtKB: Winged helix repair factor 1

Macromolecule #20: Cullin-4A

• Macromolecule: Name: Cullin-4A / type: protein_or_peptide / ID: 20 ; Details: The first three residues (Gly, Pro, Gly) are residual residues after 3C protease treatment. The coding sequence of CUL4A starts from residue 4. CUL4A K705 is modified by NEDD8.; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

GPGMADEAPR KGSFSALVGR TNGLTKPAAL AAAPAKPGGA GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEELY QAVENLCSHK VSPMLYKQLR QACEDHVQAQ ILPFREDSLD SVLFLKKINT CWQDHCRQMI MIRSIFLFLD RTYVLQNSTL PSIWDMGLEL FRTHIISDKM VQSKTIDGIL LLIERERSGE AVDRSLLRSL LGMLSDLQVY KDSFELKFLE ETNCLYAAEG QRLMQEREVP EYLNHVSKRL EEEGDRVITY LDHSTQKPLI ACVEKQLLGE HLTAILQKGL DHLLDENRVP DLAQMYQLFS RVRGGQQALL QHWSEYIKTF GTAIVINPEK DKDMVQDLLD FKDKVDHVIE VCFQKNERFV NLMKESFETF INKRPNKPAE LIAKHVDSKL RAGNKEATDE ELERTLDKIM ILFRFIHGKD VFEAFYKKDL AKRLLVGKSA SVDAEKSMLS KLKHECGAAF TSKLEGMFKD MELSKDIMVH FKQHMQNQSD SGPIDLTVNI LTMGYWPTYT PMEVHLTPEM IKLQEVFKAF YLGKHSGRKL QWQTTLGHAV LKAEFKEGKK EFQVSLFQTL VLLMFNEGDG FSFEEIKMAT GIEDSELRRT LQSLACGKAR VLIKSPKGKE VEDGDKFIFN GEFKHKLFRI KINQIQMKET VEEQVSTTER VFQDRQYQID AAIVRIMKMR KTLGHNLLVS ELYNQLKFPV KPGDLKKRIE SLIDRDYMER DKDNPNQYHY VA

UniProtKB: Cullin-4A

Macromolecule #21: E3 ubiquitin-protein ligase RBX1

• Macromolecule: Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 21 ; Details: The first three residues (Gly, Pro, Gly) are residual residues after 3C protease treatment. The coding sequence of RBX1 starts from residue 4.; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

GPGMAAAMDV DTPSGTNSGA GKKRFEVKKW NAVALWAWDI VVDNCAICRN HIMDLCIECQ ANQASATSEE CTVAWGVCNH AFHFHCISRW LKTRQVCPLD NREWEFQKYG H

UniProtKB: E3 ubiquitin-protein ligase RBX1

Macromolecule #22: NEDD8

• Macromolecule: Name: NEDD8 / type: protein_or_peptide / ID: 22 ; Details: Residue 1 (Ser) comes from linker, the coding sequence of NEDD8 starts from residue 2 (Met).; Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SMLIKVKTLT GKEIEIDIEP TDKVERIKER VEEKEGIPPQ QQRLIYSGKQ MNDEKTAADY KILGGSVLHL VLALRGG

UniProtKB: Ubiquitin-like protein NEDD8

Macromolecule #23: Template strand DNA

• Macromolecule: Name: Template strand DNA / type: dna / ID: 23 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)

Sequence

String:

GATCAAGCTC AAGCGCTCTG CTCCTTCTCC CATCCTCTCG ATGGCTATGA GATCAACTAG

Macromolecule #24: Non-template strand DNA

• Macromolecule: Name: Non-template strand DNA / type: dna / ID: 24 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)

Sequence

String:

CTAGTTGATC TCATATTTCA TTCCTACTCA GGAGAAGGAG CAGAGCGCTT GAGCTTGATC

Macromolecule #25: RNA

• Macromolecule: Name: RNA / type: rna / ID: 25
• Source (natural): Organism: Homo sapiens (human)

Sequence

String:

GAAUAUAUAU ACAAAAUCGA GAGGA

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.15 mg/mL

Buffer

pH: 7.5
Component:

Concentration	Formula	Name
20.0 mM	HEPES	HEPES
100.0 mM	NaCl	sodium chloride
2.0 mM	MgCl2	magnesium chloride
10.0 uM	ZnSO4	zinc sulfate
1.0 mM	TCEP	tris(2-carboxyethyl)phosphine

• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
• Details: The final concentration of Pol II is around 0.15 mg/ml. The other components were added in different molar ratio. This sample was glutaraldehyde crosslinked.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Slit width: 20 eV
• Details: Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13029 / Average exposure time: 3.43 sec. / Average electron dose: 50.0 e/Ų; Details: Two datasets were collected from the same sample using the same parameters.
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 2866913 / Details: Particles were combined from two datasets.
• Startup model: Type of model: OTHER
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 275539
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC